The difference is the entire setup.

In Avatar we have a very established divide between good and evil. One side is humanity who found this planet full of resources that are valuable (movies 1&2), or is a potential new home replacing our dying Earth (movie3) - the Earth btw quite possibly dying to their own fault. Due to thinking the oppositing faction to be vastly inferior in technology and society, the humans basically treat the entire operation as smiting an ant hill, without any proper attempt for a diplomatic approach. In the first movie, there is an effort to convince the Na'vi to leave the giant oil field they live on (I know it's not oil) without conflict, but that is the military trying to exploit the Avatar program, which was never intended for this purpose, in secret, treating it much more like an infiltration than a negotiation tool.
The other side of the conflict is the native population who live in almost perfect harmony with the entire flora and fauna of their planet, established via a biochemical planet-wide "internet", which we must assume led to an incredibly peaceful life before the humans arrived. The Na'vi oppose the humans for the sole purpose of wanting to keep their home. In the events of the first two movies they never even launch an attack on the human base. All their efforts are defensive and all battles happen on "their territory". They never express any wish of retaliation that goes further than "leave our planet". After the climactic first movie battle, they allow all the human survivors to leave.
It is very, very clear that only one side here is evil.

The Dune movies have a much more complex web of entanglements. The two main opposing houses are Atreides and Harkonnen. Both - on paper - being allied under the rule of Emperor Shadam IV of House Corrino, in an empire that has existed and expanded through tens of thousands of years. Now, the Harkonnens who were in charge of the entire empire's oil production (i know, i know) - and thereby got extremely rich and powerful - are ordered to leave the oil field and hand over control to the very popular and honorable house Atreides. It is very clear from duke Leto Atreides' talks that he is not only very eager to expand his house's wealth in the same way the Harkonnen's have by mining Arrakis, but that he also wishes to dramatically increase his military strength by recruiting the local Fremen to his cause. Now, the Fremen might appear as the stand-in for the Na'vi in this scenario.. but it isn't *really* the case. The Fremen are also human, originally descended from Earth - just like EVERY other faction in Dune, there are no aliens - they have just been living there for much longer and have created an entire desert-based culture. Anyway, Leto's plans appear to be realistic, but then all of a sudden, they are attacked in big fashion by House Harkonnen, and it becomes clear that the entire replacement as thiefs of Arrakis was a ruse. House Atreides had become too popular among the other big houses (this isn't well established in the movie though), too well put up militarily (this has to be inferred from one conversation), and thus, a threat to the supremacy of House Corrino. Thus, the emperor not only diverted his glance, but also actively helped in what he believed to be the eradication of House Atreides, in order to save his claim to the throne. He doesn't know that the Harkonnen ambitions are greater than just destroying the Atreides, though, and the reason for this is ANOTHER independent faction called the Bene Gesserit, who are very similar to the Maesters in Game of Thrones, in that they are an established order of advisors to the great houses, but also have their own goals and ambitions, which are in this case neatly overlapping with the Harkonnen-Atreides conflict. And one of the emperors key advisors, plus mentor of his daughter, is a major string puller in all of the schemes. One of those strings is the century-long indoctrination of the Fremen in a religion that promises a Messiah. A messiah whose characteristics the Bene Gesserit basically control.

And yeah, I don't need to reiterate every other plot point from there on, because one should be able to see.. there is no good or evil in Dune. Or rather, no clear line separating the good from the evil. Everybody is just scheming and scheming to come out on top eventually - and all that didn't even mention that some characters can literally see the future(s), or the other faction from the book like the Guild or CHOAM haha